[gmx-users] Topology file for D2O
tsjerkw at gmail.com
Tue Mar 27 08:52:47 CEST 2007
Hi Joys Yu,
I'm not exactly sure what is happening and why the mass is not
produced correctly. You could check in the .tpr file using gmxdump
whether the masses are correct there, but given the log, it probably
is not. It is possible that grompp does not read the altered
ffgmx.atp, but uses an original, unaltered one instead. You can
circumfent that by copying the altered file to your working directory.
Alternatively, and probably a bit cleaner, you can copy the file
spc.itp to d2o.itp and edit the masses there, leaving the .atp file.
In addition, you could change the residue name to D2O, which you would
also have to change in the .gro file to (sed s/SOL/D2O/ d2o.gro >
d2o-out.gro). That way, you just add a new molecule type.
On another note, you might want to use a different force field.
Although it probably shouldn't matter for pure SPC/D2O, the GMX force
field is deprecated and should not be used for production runs, unless
there are specific reasons to do so, e.g. replication of earlier
On 3/27/07, Joys Yu <joys_yu3 at yahoo.com> wrote:
> Dear all,
> I would like to do simulation of bulk heavy water
> (D2O). So first thing, I need to get the topology file
> of D2O. In fact, I would like to use SPC H2O. I just
> need to change the mass of H in H2O from 1.008 to
> I would like to use gromacs force field(#7). So I
> revised ffgms.atp. I changed the mass of water
> hydrogen from 1.008 to 2.016.
> When I use pdbtogmx to get the topology, it seems
> fine. I have a bulk heavy water, which has 674 D2O.
> Here is some of the running results from pdbtogmx:
> Now there are 674 residues with 2022 atoms
> Making bonds...
> Opening library file
> Number of bonds was 1348, now 1348
> Generating angles, dihedrals and pairs...
> There are 0 dihedrals, 0 impropers, 674 angles
> 0 pairs, 1348 bonds and 0 virtual
> Total mass 13501.164 a.m.u.
> Total charge 0.000 e
> The total mass for 674 D2O is correct: 674 * 20.03 =
> Here is the topology file that I got for D2O:
> ; File 'd2o.top' was generated
> ; By user: Joys (1002)
> ; On host: Boyang
> ; At date: Mon Mar 26 20:15:57 2007
> ; This is your topology file
> ; Generated by genbox
> ; Include forcefield parameters
> #include "ffgmx.itp"
> ; Include water topology
> #include "spc.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> ; Include generic topology for ions
> #include "ions.itp"
> [ system ]
> ; Name
> Generated by genbox
> [ molecules ]
> ; Compound #mols
> SOL 674
> Everything seems fine here. Then I want to do a MD
> simulation. I used grompp to get the .tpr. I could
> also run it. But in the .log file, I found the mass of
> the system is the mass of H2o ( about 12132) not
> I got D2O topology from pdb2gmx correctly. But it
> seems that grompp did not read in this topology.
> Can anybody kindly tell me where the problem is? What
> should I do to get D2O topology?
> Many thanks,
> Joys Yu
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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